Truthfully I would love to see this happen, but as mentioned above the length of the game would hinder the over all experience of visiting every region if it played like a traditional pokemon game. supereffective had a nice though about taking over the world... but to me that would suffer from the same cons as before; beat people up, beat more people up, beat your rival (or in this case heroes from other games), beat up the gym leader, move on and do the same thing again.
I believe something of this caliber should be treated for what it is... fan service! No, I am not talking about panty shots and shower scenes with way to much "steam", but rather giving people what they want (unless they are wanting the fore mentioned underwear and bathing scenes, then they are out of luck.) Let me explain further, but before I do I would like to say that this comes from my personal experience of wants, expectations and the wants/expectations of those whom I have discussed this very idea with. (Don't lie to me, if you played pokemon before the 3rd gen came out, then you always played a game that had all the regions in it and complained with your friends how disappointing it was when Hoenn was released by itself and how cool would it be if a pokemon game was released with every region in it.)
Okay, so most people (at least from my experience) want a game with every region in it just for the sake of because, it would be cool, they like some location in a few games and wished they could visit them all in one game, or to catch them all (which doesn't help if you consider in the core games a hand full of pokemon have never been catch-able.) So the biggest one to focus on is being able to visit said location. That will probably be the peak excitement and top the nostalgia factor. BUT WAIT! That is a lot of locations wouldn't that still suffer from the problems of people have pointed out? Yes, yes it would. So lets address that.
When you think of putting every region in one game you might think that everyone would be foaming at the mouth to play a game where EVERY LOCATION is available... But this might not be accurate, while yes having every map lovingly remade into one game would be awesome, a lot of people probably focus on their favorite location (a.k.a. the main locations) like Mt. Silver, the Space Station in Hoenn, Lumiose City, ect... It's unlikely that they are super excited to see Route 13 in Kanto any time soon. So whatever the main story is (outside of getting gym badge, or heck make battling the gym completely optional) should take the player to the more memorable locations to do challenges or quests (IE: visiting Mt. Moon to beat up 100 Zubat, Go pay your respects at the pokemon tower in Lavender Town, Look around the burned mansion in Cinnabar Island to learn something about Mew) then move on to the next region while letting the player go do what ever they want to before they move on, like battle the gyms, catch pokemon, go kill another 100 Zubat because F-YOU ZUBAT! That way the player can decide when to move on.
Let me give an example, lets say you want to travel across The States, you want to get a good feel of the location before you move on, so at each stop you spend about a week there to enjoy yourself... That would be 50 weeks!!! That sounds nice, I would love to skip work for a 50 week vacation, but after so long it wouldn't feel like a vacation any more and you would wind-up getting annoyed more that relaxed or having fun, so instead you should split the trip up into locations you want to visit, NY with the Statue of Liberty, Miami Florida, San Diego California, ect... with the freedom of making any minor stops along the way for any length of time. Just like heading from The Smoky Mountains from Tennessee to go visit that statue of a giant lady in the harbor of New York with the pit stop of Washing DC, the player could be going from Mount Moon to Lavender Town, but choose to stop at the Pokemon Fan Club in Vermilion City, something some might enjoy, but not necessary for those that don't want to go out of their way. The game could be short for those that want to go to places that they want to go to and catch what they want to, it could be long and drawn out for those that are willing to beat every gym in between quests on their journey, or any length in between based on how much the player wants to explore that particular region.
*Honestly feel free to regard all of this, it is 1 o'clock in the morning my time and I have to get up for work in 4 hours... I don't know what I'm doing right now*
Edit:Okay, 4 hours later and I'm up!
What about story? I know everyone that wants to make a game wants to have their own story added to it, make the world as they see fit. But most pokemon games have a pretty bad story... (the region/world/universe is in danger! The leader of Team "EVIL ORGANIZATION" wants to rule the region/world/universe, but only YOU and 10 year old child is the only thing standing in their way, because they have a bunch of low leveled Rattata or something,,,,) As a few youtubers have mentioned that its more about the lore in the back of the game when you go out of your way to learn a little bit more about the world of pokemon that makes the games more interesting to play. And with 7 regions to play with one could cram a ton of lore into the game for the player to find/stumble across.
*Ya... I'm up but not really awake.... If this turns out to be gibberish that just sounds good in my barley function head, then just over look this and move on with your life.*